GEOS-5 Quick Start: Difference between revisions

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Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''. Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them. The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them. The <code>cap_restart</code> file is simply one line of text with the date of the restart files in the format YYYYMMDD<space>HHMMSS. The boundary conditions/forcings are provided by symbolic links created by the run script.

The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''. It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days per segment, the internal between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time. END_DATE ~~can be changed to your end~~ date~~, or just left as is~~. ~~Commenting~~ out the <code>qsub $HOMDIR/gcm_run.j</code> at the end of the script will prevent the script from being resubmitted~~, too~~. Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.

The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''. It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days per segment, the internal between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time. Leave END_DATE alone in Fortuna 2.0 -- there is a bug that erroneously resubmits the script after this date. You can stop the run by commenting out the <code>qsub $HOMDIR/gcm_run.j</code> at the end of the script, which will prevent the script from being resubmitted. Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.

Submit the job with <code>qsub gcm_run.j</code>. You can keep track of it with <code>qstat</code> or <code>qstat | grep ''USERID''</code>, or stdout with <code>tail -f /discover/pbs_spool/''JOBID''.OU</code>, ''JOBID'' being returned by <code>qsub</code> and displayed with <code>qstat</code>. Jobs can be killed with <code>qdel ''JOBID''</code>. The standard out and standard error will be delivered as files to the working directory at the time you submitted the job.

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 Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''.   Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them.  The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them.   The <code>cap_restart</code> file is simply one line of text with the date of the restart files in the format YYYYMMDD<space>HHMMSS.  The boundary conditions/forcings are provided by symbolic links created by the run script.
-The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''.  It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days per segment, the internal between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time.  END_DATE can be changed to your end date, or just left as is.  Commenting out the <code>qsub $HOMDIR/gcm_run.j</code> at the end of the script will prevent the script from being resubmitted, too.  Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.
+The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''.  It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days per segment, the internal between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time.  Leave END_DATE alone in Fortuna 2.0 -- there is a bug that erroneously resubmits the script after this date.  You can stop the run by commenting out the <code>qsub $HOMDIR/gcm_run.j</code> at the end of the script, which will prevent the script from being resubmitted.  Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.
 Submit the job with <code>qsub gcm_run.j</code>.  You can keep track of it with <code>qstat</code> or <code>qstat | grep ''USERID''</code>, or stdout with <code>tail -f /discover/pbs_spool/''JOBID''.OU</code>, ''JOBID'' being returned by <code>qsub</code> and displayed with <code>qstat</code>.  Jobs can be killed with <code>qdel ''JOBID''</code>.  The standard out and standard error will be delivered as files to the working directory at the time you submitted the job.